[phenixbb] anisotropic refinement water hydrogens and gui

Nathaniel Echols NEchols at lbl.gov
Tue Mar 9 07:06:22 PST 2010

On Mar 9, 2010, at 11:58 AM, Christian Roth wrote:
> I did an anisotropic refinement with the gui for a 1.6 Ang. structure I think this is quite O.K. as the R-values seems to be reasonable(14/18.8).  But for comparison I want exclude waters and hydrogens explicitly from the anistropic refinement. One could do this in the command line mode via adp.individual.anisotropic ="not water and not element H. I started from the gui and modified the .eff directly by icnluding:
> adp {
>       individual {
>         isotropic = None
>         anisotropic = "not water and not element H"
> In the output pdb all waters have an anisou flag. So I assume phenix refined them anisotropically. How do I have to modify the .eff file to exclude the waters from the anisotropic refinement. 
> I would like to use the gui, because you get this nice summary output with all statistics. 
> Phenix started optionally anisotropic refinement at 1.7 Ang. As far as I understand one should keep in mind that the data to parameter ration should have certain value of app. 3 or 4. But restraints as paramters are not as solid as experimental data. Is this 1.7 Ang. borderline a rule of thumb, is there a strict rule at which point I could refine anisotropic, or maybe mixed isotropic anisotropic. 

It isn't the R-values that matter, it's how much anisotropic refinement improves them.  I always followed the advice in the SHELX FAQ: "Generally, if the drop in Rfree is less than 1 % you should revert to isotropic."  This may be too strict, but the overall message is sound.  You seem to have a rather large spread between R and R-free, which is slightly troubling (although not necessarily a deal-breaker).


As far as excluding waters goes, two suggestions: try explicitly setting the isotropic selection to the waters, and try using "resname HOH" instead of "water".  (Although I thought "water" was supposed to work too...)

Another approach would be to perform TLS refinement of the protein, which will incorporate anisotropy without greatly increasing the number of refined parameters.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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